Background <p>The coronavirus disease 2019 (COVID-19) pandemic has profoundly impacted lives worldwide, influencing the incidence and severity of health problems. This may have affected the occurrence of workers’ sickness absences. This study aims to examine the incidence of long-term sickness absences due to mental disorders from 2009 to 2022 and the impact of the COVID-19 pandemic from the beginning of the COVID-19 pandemic (2020) to the end of the COVID-19 pandemic (2022).</p> Methods <p>A retrospective observational design was employed. An anonymized record of public servants in City A with long-term sickness absences (≥ 90 days) from 2009 to 2022 was obtained. We defined 2009–2019 as the pre-COVID-19 pandemic period and 2020–2022 as the COVID-19 pandemic period. The influence of the COVID-19 pandemic on each disease category, classified using the ICD-10, was analyzed through interrupted time series analysis (ITSA) to evaluate changes in long-term sickness absences incidence before and during the COVID-19 pandemic period and the Cochran‒Armitage test to estimate trends in incidence rates over time.</p> Results <p>Mental and behavioural disorders consistently demonstrated the highest incidence rates among all disease categories, with mood disorders being the most prevalent. Trends for all diseases analyzed did not change due to the COVID-19 pandemic. However, both ITSA and the Cochran‒Armitage test revealed increasing trends for depressive states and adjustment disorders throughout the study period.</p> Conclusions <p>The COVID-19 pandemic did not influence the incidence of long-term sickness absences. However, depressive states and adjustment disorders exhibited an upward trend. This study underscores the need for tailored workplace mental health interventions to tackle the increasing stress-related illnesses, necessitating future research exploring the root causes.</p>